moldyn Goto Github PK
Name: Biomolecular Dynamics
Type: Organization
Bio: Group of Prof. Dr. G. Stock, University of Freiburg
Twitter: MolDynFR
Location: Freiburg
Name: Biomolecular Dynamics
Type: Organization
Bio: Group of Prof. Dr. G. Stock, University of Freiburg
Twitter: MolDynFR
Location: Freiburg
Jupyter notebook with 2D test potential energy landscape for performing model biased simulations combined with pathway analysis.
Robust and stable clustering of molecular dynamics simulation trajectories.
Program to run the data driven Langevin equation as described in Schaudinnus et al., Phys. Rev. Lett. 115, 050602 (2015) or Rzepiela et al. J. Chem. Phys. 141, 241102 (2014). The basic publication is Hegger and Stock, J. Chem. Phys. 130, 034106 (2009) .
Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.
dissipation corrected targeted molecular dynamics
Fast, parallelized implementation of Principal Component Analysis with constant memory consumption for large data sets.
Fastest Gephi's ForceAtlas2 graph layout algorithm implemented for Python and NetworkX
Selecting Features for Markov Modeling: A Case Study on HP35
Benchmarking dimensionality reduction methods and clustering on HP35-DESRES
DESRES trajectory of wild type HP-35 at 360K
Includes C++ code to run Markovian Langevin equations in units compatible with the dcTMD correction scripts available at www.moldyn.uni-freiburg.de/software/software.html. In addition, a jupyter notebook can be found which estimates the error of rates at 300 K from T-boosting calculations.
Correlation-based feature selection of Molecular Dynamics simulations
Helper function for Markov State Models
Finding pathways from an Markov State Model
Generalized Kraskov Estimator for Normalized Mutual Information
An example python packaging
The ramacolor script produce plots as proposed in Sittel et al., J. Chem. Theory Comput 12, 2426 (2016)
Includes implementations of the data-driven Langevin equation with and without rescaling of the friction. Includes also data-driven Langevin codes which work with pre-averaged data. Finally, programs can be found to produce Markovian and generalized Langevin dynamics in case the fields are already known. The generalized Langevin equation assumes a mono-exponential memory kernel.
Tutorial for the usage of the dcTMD approach and Langevin simulations employing the trypsin-benzamidine complex as example.
Machine-Learning analysis of large data sets from molecular dynamics simulation
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.